| 1. |
Yusuke Yagi, Takamasa Teramoto, Shuji Kaieda, Takayoshi Imai, Tadamasa Sasaki, Maiko Yagi, Nana Maekawa, Takahiro Nakamura, Construction of a Versatile, Programmable RNA-Binding Protein Using Designer PPR Proteins and Its Application for Splicing Control in Mammalian Cells, Cells, https://doi.org/10.3390/cells11223529, 2022.11. |
| 2. |
Mizuho Ichinose, Masuyo Kawabata, Yumi Akaiwa, Yasuka Shimajiri, Izumi Nakamura, Takayuki Tamai, Takahiro Nakamura, Yusuke Yagi, Bernard Gutmann, U-to-C RNA editing by synthetic PPR-DYW proteins in bacteria and human culture cells, Communications biology, 2022.09. |
| 3. |
Kobayashi T, Yagi Y, Nakamura T, Development of Genome Engineering Tools from Plant-Specific PPR Proteins Using Animal Cultured Cells., Methods Mol Biol. , 10.1007/978-1-4939-4931-1_11, 1469, 147-155, 2016.08. |
| 4. |
Kazama T, Itabashi E, Fujii S, Nakamura T, Toriyama K, Mitochondrial ORF79 levels determine the timing of pollen abortion in cytoplasmic male sterile, The Plant Journal, doi: 10.1111/tpj.13135, 85, 6, 707-716, 2016.03. |
| 5. |
Yagi Y, Shirakawa M, Nakamura T, The challenges faced by EditForce Inc., to go beyond genome editing, Nature, Sponsor feature, 2015.12, EditForce Inc., established in May 2015, provides an alternative option to genome editing and a novel tool for versatile RNA editing at the genomic scale, called ‘transcriptome editing’, based on pentatricopeptide repeat (PPR) protein engineering technologies. Our core technologies have been invented at Kyushu University, Japan. The company is located in Fukuoka city in Kyushu, a southwestern island of Japan. EditForce is an innovative company in the post-genomic era. Our mission is to provide novel DNA/RNA operating tools to understand and modify various living entities and to translate our PPR technologies in various biological industries, including the pharmaceutical and agricultural industries.. |
| 6. |
Kenji Okuda, Harumi Shoki, Miho Arai, Toshiharu Shikanai, Ian Small, Takahiro Nakamura, Quantitative analysis of motifs contributing to the interaction between PLS-subfamily members and their target RNA sequences in plastid RNA editing, PLANT JOURNAL, 10.1111/tpj.12687, 80, 5, 870-882, 2014.12, In plant organelles, RNA editing alters specific cytidine residues to uridine in transcripts. Target cytidines are specifically recognized by pentatricopeptide repeat (PPR) proteins of the PLS subfamily, which have additional C-terminal E or E-DYW motifs. Recent in silico analysis proposed a model for site recognition by PLS-subfamily PPR proteins: one-PPR motif to one-nucleotide correspondence with the C-terminal last S motif aligning to the nucleotide at position -4 with respect to the editing site. Here we show quantitative biochemical data on site recognition by four PLS-subfamily proteins: CRR28 and OTP85 are DYW-class members while CRR21 and OTP80 are E-class members. The minimal RNA segments required for high affinity binding by these PPR proteins were experimentally determined. The results were generally consistent with the in silico based model. However, we clarified that several PPR motifs, including the C-terminal L2 and S motifs of CRR21 and OTP80, are dispensable for the RNA binding, suggesting distinct contributions of each PPR motif to site recognition. We also demonstrate that the DYW motif interacts with the target C and its 5′ proximal region (-3 to 0), whereas the E motif is not involved in binding.. |
| 7. |
Yusuke Yagi, Takahiro Nakamura, Ian Small, The potential for manipulating RNA with pentatricopeptide repeat proteins, PLANT JOURNAL, 10.1111/tpj.12377, 78, 5, 772-782, 2014.06, The pentatricopeptide repeat (PPR) protein family, particularly prevalent in plants, includes many sequence-specific RNA binding proteins involved in all aspects of organelle RNA metabolism including RNA stability, processing, RNA editing, and translation. PPR proteins consist of a tandem array of 2-30 PPR motifs each of which aligns to one nucleotide in the RNA target. The amino acid side-chains at 2-3 specific positions in each motif confer nucleotide specificity in a predictable and programmable manner. Thus, PPR proteins appear to provide an extremely promising opportunity to create custom RNA binding proteins with tailored specificity. We summarize recent progress in understanding RNA recognition by PPR proteins with a particular focus on potential applications of PPR-based tools for manipulating RNA, and on the challenges that remain to be overcome before these tools can be routinely used by the scientific community.. |
| 8. |
Tomohiko Kazama, Yusuke Yagi, Kinya Toriyama, Takahiro Nakamura, Heterogeneity of the 5 '-end in plant mRNA may be involved in mitochondrial translation, FRONTIERS IN PLANT SCIENCE, 10.3389/fpls.2013.00517, 4, 517, 2013.12. |
| 9. |
Yusuke Yagi, Makoto Tachikawa, Hisayo Noguchi, Soichiro Satoh, Junichi Obokata, Takahiro Nakamura, Pentatricopeptide repeat proteins involved in plant organellar RNA editing, RNA BIOLOGY, 10, 9, 1419-1425, 2013.09. |
| 10. |
Yusuke Yagi, Shimpei Hayashi, Keiko Kobayashi, Takashi Hirayama, Takahiro Nakamura, Elucidation of the RNA recognition code for pentatricopeptide repeat proteins involved in organelle RNA editing in plants., PLoS ONE, 10.1371/journal.pone.0057286, 8, 3, e57286, 2013.03, Pentatricopeptide repeat (PPR) proteins are eukaryotic RNA-binding proteins that are commonly found in plants. Organelle transcript processing and stability are mediated by PPR proteins in a gene-specific manner through recognition by tandem arrays of degenerate 35-amino-acid repeating units, the PPR motifs. However, the sequence-specific RNA recognition mechanism of the PPR protein remains largely unknown. Here, we show the principle underlying RNA recognition for PPR proteins involved in RNA editing. The distance between the PPR-RNA alignment and the editable C was shown to be conserved. Amino acid variation at 3 particular positions within the motif determined recognition of a specific RNA in a programmable manner, with a 1-motif to 1-nucleotide correspondence, with no gap sequence. Data from the decoded nucleotide frequencies for these 3 amino acids were used to assign accurate interacting sites to several PPR proteins for RNA editing and to predict the target site for an uncharacterized PPR protein.. |
| 11. |
Takahiro Nakamura, Yusuke Yagi, Keiko Kobayashi, Mechanistic Insight into Pentatricopeptide Repeat Proteins as Sequence-Specific RNA-Binding Proteins for Organellar RNAs in Plants, Plant Cell Physiol, 53, 7, 1171-1179, 2012.06, The pentatricopeptide repeat (PPR) protein family is highly expanded in terrestrial plants. Arabidopsis contains 450 PPR genes, which represents 2% of the total protein-coding genes. PPR proteins are eukaryote-specific RNA-binding proteins implicated in multiple aspects of RNA metabolism of organellar genes. Most PPR proteins affect a single or small subset of gene(s), acting in a gene-specific manner. Studies over the last 10 years have revealed the significance of this protein family in coordinated gene expression in different compartments: the nucleus, chloroplast, and mitochondrion. Here, we summarize recent studies addressing the mechanistic aspect of PPR proteins.. |
| 12. |
Maki Murayama, Shimpei Hayashi1, Noriyuki Nishimura1, Mayumi Ishide, Keiko Kobayashi, Yusuke Yagi, Tadao Asami, Takahiro Nakamura, Kazuo Shinozaki, Takashi Hirayama, Isolation of Arabidopsis ahg11, a weak ABA hypersensitive mutant defective in nad4 RNA editing , J. Exp. Bot., 10.1093/jxb/ers188, 2012.06, The phytohormone abscisic acid (ABA) plays pivotal roles in the regulation of developmental and environmental responses in plants. Identification of cytoplasmic ABA receptors enabled the elucidation of the main ABA signaling pathway, connecting ABA perception to either nuclear events or the action of several transporters. However, the physiological functions of ABA in cellular processes largely remain unknown. To obtain greater insight into the ABA response, we performed genetic screening to isolate ABA-related mutants of Arabidopsis and isolated several novel ABA-hypersensitive mutants. We further characterized one of those mutants—ahg11. Map-based cloning showed that AHG11 encodes a PPR type protein, which has potential roles in RNA editing. An AHG11-GFP fusion protein indicated that AHG11 mainly localized to the mitochondria. Consistent with this observation, the nad4 transcript, which normally undergoes RNA editing, lacks a single RNA editing event conferring a conversion of an amino acid residue in ahg11 mutants. The geminating ahg11 seeds have higher levels of reactive oxygen species responsive genes. Presumably partial impairment of mitochondrial function caused by an amino acid conversion in one of the Complex I components induces redox imbalance, which in turn confers abnormal response to the plant hormone. . |
| 13. |
Kobayashi K, Kawabata M, Hisano K, Kazama T, Matsuoka K, Sugita M, Nakamura T, Identification and characterization of the RNA binding surface of the pentatricopeptide repeat protein, Nucleic Acids Res., 40, 2712-2723, 2012.03, 葉緑体とミトコンドリアの遺伝子発現は核にコードされる遺伝子によって転写後のRNAのレベルで大きく制御されている。最近の研究で、植物で特有に大きなファミリーを形成するPPR蛋白質が配列特異的なRNA結合蛋白質として、前述のオルガネラRNA代謝に重要な役割を担うことが明らかになってきた。PPR蛋白質中の複数のPPRモチーフ(35アミノ酸）の繰り返しがRNA結合に働くと推測されているが、その詳細は明らかでない。我々はここに、PPR蛋白質のRNA結合の分子基盤を示した。まず、Pfamにおけるモチーフの定義がPPRモチーフのRNA結合ユニットとしての働きを正しく示すことを明らかにした。また、2個のPPRモチーフからなる一連の組換え蛋白質を用いた生化学的、計算科学的な解析から、5個のアミノ酸（1、4、8、12、ii(-2））がPPRモチーフのRNA結合表面を形成することを明らかにした。SELEX法などにより、配列特異的なRNA結合を解析したところ、PPRとRNAの相互作用の親和性、配列特異性に関わることをいくつかの特徴的なアミノ酸を見いだした。. |
| 14. |
Okuda K, Chateigner-Boutin AL, Nakamura T, Delannoy E, Sugita M, Myouga F, Motohashi R, Shinozaki K, Small I, Shikanai T, Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts, Plant Cell, 21, 146-156, 2009.05. |
| 15. |
Nakamura T, Sugita M, A conserved DYW domain of the pentatricopeptide repeat protein possesses a novel endo-ribonuclease activity, FEBS Lett., 582, 163-168, 2008.12. |
| 16. |
Kazama T, Nakamura T, Watanabe M, Sugita M, Toriyama K, Suppression mechanism of mitochondrial ORF79 accumulation by Rf1 protein in BT-type cytoplasmic male sterile rice, Plant J., 55, 37661-7, 2008.08. |
| 17. |
Okuda K, Nakamura T, Sugita M, Shimizu T, Shikanai T, A pentatricopeptide repeat protein is a site recognition factor in chloroplast RNA editing, J. Biol. Chem., 281, 37661-7, 2006.12. |
